Related papers: The MOLDY short-range molecular dynamics package
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Modern LLM service providers increasingly rely on autoscaling and parallelism reconfiguration to respond to rapidly changing workloads, but cold-start latency remains a major bottleneck. While recent systems have reduced model weight…
This paper presents a comprehensive comparison of three dominant parallel programming models in High Performance Computing (HPC): Message Passing Interface (MPI), Open Multi-Processing (OpenMP), and Compute Unified Device Architecture…
GPU-based HPC clusters are attracting more scientific application developers due to their extensive parallelism and energy efficiency. In order to achieve portability among a variety of multi/many core architectures, a popular choice for an…
Software developers must adapt to keep up with the changing capabilities of platforms so that they can utilize the power of High- Performance Computers (HPC), including exascale systems. OpenMP, a directive-based parallel programming model,…
COSA is a novel CFD system based on the compressible Navier-Stokes model for unsteady aerodynamics and aeroelasticity of fixed structures, rotary wings and turbomachinery blades. It includes a steady, time domain, and harmonic balance flow…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We introduce PULSEDYN, a particle dynamics program in $C++$, to solve many-body nonlinear systems in one dimension. PULSEDYN is designed to make computing accessible to non-specialists in the field of nonlinear dynamics of many-body systems…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
Multicore has emerged as a typical architecture model since its advent and stands now as a standard. The trend is to increase the number of cores and improve the performance of the memory system. Providing an efficient multicore…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
Multimodal large language models (MLLMs) extend the capabilities of large language models (LLMs) by combining heterogeneous model architectures to handle diverse modalities like images and audio. However, this inherent heterogeneity in MLLM…
We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…